D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings

Autor: Scott D. Bembenek, W. Patrick Walters, Neysa Nevins, Zied Gaieb, Michael K. Gilson, Michael Chiu, Chenghua Shao, Stephen K. Burley, Tara Mirzadegan, Rommie E. Amaro, Conor Parks, Millard H. Lambert, Michael K. Ameriks, Huanwang Yang

Publikováno v: Journal of computer-aided molecular design, vol 33, iss 1

The Drug Design Data Resource aims to test and advance the state of the art in protein-ligand modeling, by holding community-wide blinded, prediction challenges. Here, we report on our third major round, Grand Challenge 3 (GC3). Held 2017–2018, GC3

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7d1cb9830555d3a9ff49c469cf3b529f
https://doi.org/10.1007/s10822-018-0180-4

Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges

Autor: Bentley M. Wingert, Carlos J. Camacho, Rick Oerlemans

Publikováno v: Journal of Computer-Aided Molecular Design, 32(1), 287-297. SPRINGER

The goal of virtual screening is to generate a substantially reduced and enriched subset of compounds from a large virtual chemistry space. Critical in these efforts are methods to properly rank the binding affinity of compounds. Prospective evaluati

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a4486b920723b435e70e11b8b9f1c41f
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5771500/pdf/nihms906756.pdf

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation

Autor: Daan P. Geerke, Nico P. E. Vermeulen, Marc van Dijk, Eko Aditya Rifai

Publikováno v: Journal of Computer-aided Molecular Design
Journal of Computer-Aided Molecular Design
Journal of Computer-aided Molecular Design, 32(1), 239-249. Springer Netherlands
Rifai, E A, van Dijk, M, Vermeulen, N P E & Geerke, D P 2017, ' Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation : application to the D3R Grand Challenge 2 ', Journal of Computer-aided Molecular Design, vol. 32, no. 1, pp. 239-249 . https://doi.org/10.1007/s10822-017-0055-0

Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::580c9a18f6878d4971290234f09a515f
https://doi.org/10.1007/s10822-017-0055-0

Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations

Autor: Eddy Elisée, Edithe Selwa, Agustin Zavala, Bogdan I. Iorga

Publikováno v: Journal of Computer-Aided Molecular Design
Journal of Computer-Aided Molecular Design, Springer Verlag, 2018, 32 (1), pp.273-286. ⟨10.1007/s10822-017-0054-1⟩

This work was supported by the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) [grant number ANR-10-LABX-33], by the JPIAMR transnational project DesInMBL [grant number ANR-14-JAMR-0002] and by the Région Ile

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fdf2f3d4bdadc7a82ef10160bacfc36c
https://hal.archives-ouvertes.fr/hal-03164746/file/Selwa_JComputAidedMolDes_2018_273.pdf

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